Encoding and decoding of array sensors utilizing nanocrystals

• US 20030175773A1
• Filed: 12/31/2002
• Published: 09/18/2003
• Est. Priority Date: 05/20/1999
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Zhao, Chanfeng, Chee, Mark S., Barnard, Steven M.
• Granted Patent: US 6,890,764 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B82Y 15/00 Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
• CPC Class Codes: G01N 21/6428 Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• CPC Class Codes: G01N 33/587 Nanoparticles
• CPC Class Codes: G01N 33/588 with semiconductor nanocrystal label, e.g. quantum dots
• CPC Class Codes: Y10S 436/805 Optical property
• CPC Class Codes: Y10S 436/823 Immunogenic carrier or carrier per se
• CPC Class Codes: Y10S 977/70 Nanostructure
• CPC Class Codes: Y10S 977/776 Ceramic powder or flake
• CPC Class Codes: Y10S 977/789 in array format
• CPC Class Codes: Y10S 977/792 Nucleic acid array, e.g. human genome array
• CPC Class Codes: Y10S 977/795 Composed of biological material
• CPC Class Codes: Y10S 977/898 Enzymatic
• CPC Class Codes: Y10S 977/902 Specified use of nanostructure
• CPC Class Codes: Y10S 977/904 for medical, immunological, body treatment, or diagnosis
• CPC Class Codes: Y10S 977/915 Therapeutic or pharmaceutical composition

Abstract

Described herein are assays and components for encoding and decoding microspheres. Each assay or component described utilizes at least one nanocrystal.

Claims

1. A composition comprising:

a) a substrate with a surface comprising discrete sites; and

b) a population of microspheres distributed on said sites, wherein at least one of said microspheres comprises a nanocrystal.

2. A composition according to claim 1 wherein said nanocrystal is embedded in said microsphere.

3. A composition according to claim 1 wherein said nanocrystal is sealed into porous silica using the sol-gel polymerization process.

4. A composition according to claim 1 wherein said nanocrystal is attached to said microsphere.

5. A composition according to claim 1 wherein said microsphere comprising said nanocrystal further comprises at least one additional nanocrystal.

6. A composition according to claim 1 wherein at least a plurality of said microspheres comprises a nanocrystal.

7. A composition according to claim 1 wherein at least two microspheres comprise an optical signature which differ from one another.

8. A composition according to claim 1 wherein said microspheres comprise bioactive agents.

9. A composition according to claim 8 wherein said bioactive agents comprise nucleic acids.

10. A composition according to claim 8 wherein said bioactive agents comprise proteins.

11. A composition according to claim 10 wherein said proteins are selected from the group consisting of enzymes and antibodies.

12. A composition according to claim 1 wherein said population of microspheres comprises at least a first and a second subpopulation comprising:

i) a a first and a second bioactive agent, respectively; and

ii) a first and a second optical signature, respectively, capable of identifying each bioactive agent, wherein at least one of said optical signatures comprises said nanocrystal.

13. A composition according to claim 12 wherein at least one of said optical signatures comprises at least two nanocrystals.

14. An array composition comprising:

a) a substrate with a surface comprising discrete sites; and

b) a population of microspheres comprising at least a first and a second subpopulation,

wherein each subpopulation comprises a bioactive agent bound to a target analyte comprising a nanocrystal, wherein said microspheres are distributed on said surface.

17. A composition according to claim 14 or 15 wherein said bioactive agents are nucleic acids.

18. A composition according to claim 14 or 15 wherein said bioactive agents are proteins.

15. An array composition comprising:

a) a substrate with a surface comprising discrete sites; and

b) a population of microspheres comprising at least a first and a second subpopulation, wherein each subpopulation comprises;

i) a bioactive agent; and

ii) an identifier binding ligand bound to a decoder binding ligand comprising a nanocrystal such that the identification of the bioactive agent can be elucidated;

wherein said microspheres are distributed on said surface.

16. An array composition comprising:

a) a substrate with a surface comprising discrete sites; and

b) a population of microspheres comprising at least a first and a second subpopulation, wherein each subpopulation comprises a bioactive agent bound to a decoder binding ligand comprising a nanocrystal, wherein said microspheres are distributed on said surface.

19. A method of making a composition comprising:

a) forming a surface comprising individual sites on a substrate;

b) distributing microspheres on said surface such that said individual sites contain microspheres, wherein said microspheres comprise an optical signature, wherein at least one optical signature comprises at least one nanocrystal.

20. A method of making a composition comprising:

a) forming a surface comprising individual sites on a substrate;

b) distributing microspheres on said surface such that said individual sites contain microspheres, wherein said microspheres comprise at least a first and a second subpopulation each comprising;

i) a bioactive agent; and

ii) an optical signature capable of identifying said bioactive agent, wherein at least one optical signature comprises at least one nanocrystal.

21. A method of determining the presence of a target analyte in a sample comprising:

a) contacting said sample with a composition comprising;

i) a substrate with a surface comprising discrete sites; and

ii) a population of microspheres comprising at least a first and a second subpopulation each comprising;

1) a bioactive agent; and

2) an optical signature capable of identifying said bioactive agent;

wherein said microspheres are distributed on said surface such that said discrete sites contain microspheres and wherein at least one of said optical signatures comprises at least one nanocrystal; and

b) determining the presence or absence of said target analyte.

22. A method according to claim 21 further comprising identifying the location of each bioactive agent on said substrate.

23. A method of determining the presence of a target analyte comprising an optical signature comprising at least one nanocrystal in a sample comprising:

a) contacting said sample with a composition comprising;

i) a substrate with a surface comprising discrete sites; and

ii) a population of microspheres comprising at least a first and a second subpopulation each comprising a bioactive agent;

wherein said microspheres are distributed on said surface such that said discrete sites contain microspheres; and

b) determining the presence or absence of said target analyte.

24. A method of determining the presence of a target analyte in a sample comprising:

a) contacting said sample with a composition comprising;

i) a substrate with a surface comprising discrete sites; and

ii) a population of microspheres comprising at least a first and a second subpopulation each comprising;

1) a bioactive agent; and

2) an identifier binding ligand that will bind a decoder binding ligand comprising an optical signature comprising a nanocrystal such that the identification of the bioactive agent can be elucidated;

wherein said microspheres are distributed on said surface such that said discrete sites contain microspheres;

b) contacting said sample with a plurality of said decoder binding ligands; and

c) determining the presence or absence of said target analyte.

25. A method of decoding an array composition comprising

a) providing an array composition comprising:

i) a substrate with a surface comprising discrete sites; and

ii) a population of microspheres comprising at least a first and a second subpopulation, wherein each subpopulation comprises a bioactive agent;

wherein said microspheres are distributed on said surface;

b) adding a plurality of decoding binding ligands comprising optical signatures to said array composition to identify the location of at least a plurality of the bioactive agents, wherein at least one of said optical signatures comprises a nanocrystal.

26. A method according to claim 25 wherein at least one subpopulation of microspheres comprises an identifier binding ligand to which a decoding binding ligand can bind.

27. A method according to claim 25 wherein said decoding binding ligands bind to said bioactive agents.

28. A method according to claim 25 wherein the location of each subpopulation is determined.

29. A method of making a composition comprising:

a) adhering nanocrystals to porous silica; and

b) sealing the pores of said silica using the sol-gel polymerization process.